Genetic Diversity and Relationship of Domestic Buffalo and Cattle Breeds and Crossbreeds (Subfamily Bovinae) in the Philippines Based on the Cytochrome C Oxidase I (COI) Gene Sequence

Orville L. Bondoc

Abstract


DNA barcodes (i.e., cytochrome c oxidase subunit I or COI in the mitochondrial genome) obtained from 12 buffalo and 17 cattle breeds and crossbreeds (Subfamily Bovinae) in the Philippines were analyzed using the Neighbour-Joining method based on Kimura 2-parameter model in MEGA5. Mean genetic diversity in COI sequences was higher among buffalo breeds (6.4%) than among cattle breeds (1.9%). Average genetic distance between buffaloes and cattle was 0.179 ± 0.017 units. Based on 637 COI positions, average genetic distance among river-type Murrah breeds (i.e., d = 0.104 ± 0.011) was higher than among swamp-type Philippine carabaos (i.e., d = 0.017 ± 0.003). Average genetic distance among crossbred dairy buffaloes was 0.082 ± 0.009 units. Based on 631 COI positions, average genetic distance among breeds in each cattle group was low, i.e., native cattle strains (d = 0.011 ± 0.003), purebred cattle (d = 0.022 ± 0.004) and crossbred dairy cattle (d = 0.026 ± 0.004). Our results indicate that DNA barcodes can be effective in differentiating between domestic buffaloes and cattle, but not between cattle breeds and crossbreeds. DNA barcodes may also be used to differentiate among Murrah breeds from different countries and between river-type and swamp-type buffaloes, but not among Philippine carabaos sampled from six provinces in three islands. COI sequences should be determined from more domestic buffalo and cattle breeds and crossbreeds. An expanded library of mitochondrial COI sequences, in addition to phenotypic performance standards and pedigree records, may be used to improve local programs related to food authentication, buffalo importation, genetic improvement and conservation, and protection of diversity.

Key Words: DNA barcodes, domestic water buffalo and cattle, evolutionary analysis, genetic diversity

Abbreviations: COI – cytochrome c oxidase subunit I, K2P model – Kimura 2-parameter model, NJ tree – Neighbour-Joining tree, MEGA5 – Molecular Evolutionary Genetics Analysis 5 software program


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